Monoclonal polony generation using nucleic acid supramolecular structures

Abstract

Provided herein are structures and methods for generating monoclonal clusters of a target oligonucleotide in a solution using a first nucleic acid supramolecular structure. In some cases, the target oligonucleotide is released from a second nucleic acid supramolecular structure. In some cases. the first and second nucleic acid supramolecular structure independently comprise DNA origami. In certain cases, the nucleic acid supramolecular structures may be coated in a hydrogel matrix. In other cases, the hydrogel matrix may be omitted. The monoclonal clusters created in solution using the disclosed structures and techniques may be immobilized on a substrate to facilitate subsequent processes performed on the monoclonal clusters.

1 . A hydrogel particle, comprising:
 a first nucleic acid supramolecular structure including a first chemically reactive group having an affinity to a target oligonucleotide;   a hydrogel matrix formed around the first nucleic acid supramolecular structure;   a crosslinking agent to the hydrogel matrix disposed around the first nucleic acid supramolecular structure to form a hydrogel particle;   a plurality of primers attached to the hydrogel particle and configured to facilitate amplification of the target oligonucleotide; and   a second nucleic acid supramolecular structure comprising the target oligonucleotide and linked to the first chemically reactive group through the affinity of the first chemically reactive group to the target oligonucleotide;   wherein a link between the target oligonucleotide and the second supramolecular structure is configured to be cleaved by a trigger.   
     
     
         2 . The hydrogel particle of  claim 1 , wherein the link between the target oligonucleotide and the second supramolecular structure is configured to be cleaved by the trigger in the absence of an analyte molecule. 
     
     
         3 . The hydrogel particle of  claim 2 , wherein the link between the target oligonucleotide and the second supramolecular structure is configured to be cleaved by a deconstructor molecule. 
     
     
         4 . The hydrogel particle of  claim 2 , further comprising the analyte molecule and a plurality of amplified copies of the target oligonucleotide attached to the primers. 
     
     
         5 . The hydrogel particle of  claim 1 , wherein the link between the target oligonucleotide and the second supramolecular structure is configured to be cleaved by the trigger in the presence of an analyte molecule bound to the target oligonucleotide. 
     
     
         6 . The hydrogel particle of  claim 5 , wherein the link between the target oligonucleotide and the second supramolecular structure is configured to be cleaved by a deconstructor molecule. 
     
     
         7 . The hydrogel particle of  claim 5 , further comprising the analyte molecule, and wherein amplified copies of the target oligonucleotide are not generated. 
     
     
         8 . The hydrogel particle of  claim 5 , further comprising a capture molecule linked to the second supramolecular structure and configured to bind to the analyte molecule such that in the presence of the analyte molecule, the target oligonucleotide is bound to the second supramolecular structure through binding of both the capture molecule and the target oligonucleotide to the analyte molecule. 
     
     
         9 . The hydrogel particle of  claim 8 , further comprising the analyte molecule and a plurality of amplified copies of the target oligonucleotide attached to the primers. 
     
     
         10 . The hydrogel particle of  claim 1 , wherein the first nucleic acid supramolecular structure further comprises a second chemically reactive group having an affinity to a binding molecule associated with a substrate. 
     
     
         11 . A method for forming a monoclonal cluster of a target oligonucleotide on a hydrogel particle, comprising:
 forming a hydrogel matrix around a first nucleic acid supramolecular structure comprising a first chemically reactive group having an affinity to a target oligonucleotide;   providing a crosslinking agent to the hydrogel matrix around the first nucleic acid supramolecular structure to form a hydrogel particle;   incubating the hydrogel particle with a second nucleic acid supramolecular structure comprising the target oligonucleotide, thereby facilitating capture of the target oligonucleotide by the first chemically reactive group;   providing a trigger to cleave a link between the target oligonucleotide and the second supramolecular structure; and   providing conditions for amplification of the target oligonucleotide.   
     
     
         12 . The method of  claim 11 , wherein the trigger is configured to cleave the link between the target oligonucleotide and the second supramolecular structure in the absence of an analyte molecule. 
     
     
         13 . The method of  claim 12 , wherein the trigger comprises a deconstructor molecule. 
     
     
         14 . The method of  claim 12 , further comprising detecting the analyte molecule based on whether copies of the target oligonucleotide are formed on the hydrogel particle. 
     
     
         15 . The method of  claim 11 , wherein the trigger is configured to cleave the link between the target oligonucleotide and the second supramolecular structure in the presence of an analyte molecule. 
     
     
         16 . The method of  claim 15 , wherein the trigger comprises a deconstructor molecule. 
     
     
         17 . The method of  claim 15 , further comprising detecting the analyte molecule based on lack of amplification of the target oligonucleotide. 
     
     
         18 . The method of  claim 15 , wherein the second supramolecular structure comprises a capture molecule configured to bind to the analyte molecule, and wherein in the presence of the analyte molecule, the target oligonucleotide remains bound to the second supramolecular structure after providing the trigger, through binding of both the capture molecule and the target oligonucleotide to the analyte molecule. 
     
     
         19 . The method of  claim 18 , further comprising detecting the analyte molecule based on whether copies of the target oligonucleotide are formed on the hydrogel particle. 
     
     
         20 . The method of  claim 11 , wherein the first nucleic acid supramolecular structure further comprises a second chemically reactive group having an affinity to a binding molecule associated with a substrate.